gtscript documentation

# `gtscript` documentation

This document describes the `gtscript` API. `gtscript` is basically Lua (an embeddable scripting language) plus parts of the GenomeTools C libraries exported to Lua. Because the GenomeTools binary `gt` contains an embedded Lua interpreter, `gtscript` files can be executed with the `gt` binary. The parts of the GenomeTools C libraries exported to Lua (the `gtscript` API) are described here, for a documentation of Lua itself and its APIs, please refer to the Lua reference manual.

See the index for an alphabetical list of all available interfaces.

## Notes

- You have to add `require 'gtlua'` to your script in order to load the parts of the `gtscript` API which are implemented in `gtscript` itself.
- By default, all functions of the `gtscript` API are contained in the `gt` table. That is, you have to prepend all functions calls with ```gt.`''. For example, write `gt.show()` to call the `show()` function documented below. You can use `gt.export()` or `gt.re()` to export the `gt` table to the global environment, which makes the prepending unnecessary (but clutters your global environment).
- If a function is documented as ``returns an array'', this means that the function returns a table where only consecutive integer keys from 1 on are used and which can be traversed with the `ipairs()` function.

## Classes

- Alphabet
- Bittab
- CDSStream
- CSAStream
- Canvas
- CommentNode
- Diagram
- FeatureIndex
- FeatureNode
- FeatureNodeIterator
- FeatureStream
- FeatureVisitor
- GFF3InStream
- GFF3OutStream
- GFF3Visitor
- GenomeNode
- GenomeStream
- Imageinfo
- Layout
- MetaNode
- Range
- RegionMapping
- RegionNode
- ScoreMatrix
- SequenceNode
- StreamEvaluator
- translate

## Modules

## Sole functions

`rand_max(val)`

Returns a random number between 0 and `val`.

`reload()`

Reload `gt` module.

`export()`

Export the content of `gt` table to the global environment.

`display(filename)`

Call external 'display' program for file `filename`.

`show_table(tbl)`

Show all keys and values of table `tbl`.

`show(all)`

Show content of the `gt` table.

`re()`

Reload the `gt` module and export its content to the global environment.

`features_contain_marked(features)`

Returns true if the given array of `features` contains a marked feature, false otherwise.

`features_show(features)`

Print the given array of `features` to stdout.

`features_get_marked(features)`

Return all marked `features` (an array) as an array or nil if `features` contains no marked features.

`features_show_marked(features)`

Print all marked `features` (an array) to stdout.

`features_mRNAs2genes(in_features)`

Return an array of genome features which contains a separate gene feature for each mRNA in `in_features`.

`features_extract_sequences(features, type, join, region_mapping)`

Return an array with the sequences of the given features.

## Class Alphabet

`alphabet_new_protein()`

Return a new protein alphabet.

`alphabet_new_dna()`

Return a new DNA alphabet.

`alphabet_new_empty()`

Return an empty alphabet.

`alphabet:add_mapping(characters)`

Add the mapping of all given `characters` to the given `alphabet`. The first character is the result of subsequent `alphabet:decode()` calls.

`alphabet:add_wildcard(characters)`

Add `wildcard` to `alphabet`.

`alphabet:decode(code)`

Return a string containing the decoded character of the `code` number.

`alphabet:size()`

Return the size of `alphabet` as a number.

## Class Bittab

`bittab_new(num_of_bits)`

Returns a bittab with `num_of_bits` many bits.

`bittab:set_bit(bit)`

Set `bit` in `bittab`.

`bittab:unset_bit(bit)`

Unset `bit` in `bittab`.

`bittab:complement(src)`

Store the complement of bittab `src` in `bittab`. `bittab` and `src` must have the same size.

`bittab:equal(src)`

Set `bittab` equal to bittab `src`. `bittab` and `src` must have the same size.

`bittab:and_equal(src)`

Set `bittab` equal to the bitwise AND of `bittab` and `src`. `bittab` and `src` must have the same size.

`bittab:bit_is_set(bit)`

Returns true if `bit` is set in `bittab`, false otherwise.

## Class CDSStream

`cds_stream_new(in_stream, region_mapping)`

Returns a new CDS (coding sequence) stream object (a genome stream) which uses genome stream `in_stream` as input. The CDS stream adds CDS features to exon features in `in_stream`. The given `region_mapping` is used to map the sequence regions given in `in_stream` to the actual sequence files necessary for computing the coding sequences.

## Class CSAStream

`csa_stream_new(in_stream, join)`

Returns a new CSA (consensus spliced alignment) stream object (a genome stream) which uses genome stream `in_stream` as input. The CSA stream replaces spliced alignments with computed consensus spliced alignments. The optional `join` parameters sets the length for the spliced alignment clustering (default: 300).

## Class Canvas

`canvas_cairo_file_new_png(width, imageinfo)`

Return a Canvas object which acts as a PNG drawing surface of width `width` to be passed to rendering functions as a visitor. An `imageinfo` object is filled with coordinate information if given. If not needed, pass nil as `imageinfo`.

`canvas_cairo_file_new_pdf(width, imageinfo)`

Return a Canvas object which acts as a PDF drawing surface of width `width` to be passed to rendering functions as a visitor. An `imageinfo` object is filled with coordinate information if given.

`canvas_cairo_file_new_ps(width, imageinfo)`

Return a Canvas object which acts as a PS drawing surface of width `width` to be passed to rendering functions as a visitor. An `imageinfo` object is filled with coordinate information if given.

`canvas_cairo_file_new_svg(width, imageinfo)`

Return a Canvas object which acts as a SVG drawing surface of width `width` to be passed to rendering functions as a visitor. An `imageinfo` object is filled with coordinate information if given.

`canvas:to_file(filename)`

Creates an image file with the given `filename` which contains the contents of the canvas (only for objects created with `canvas_cairo_file_new_*()`).

## Class CommentNode

`comment_node_new(comment)`

Returns a new comment node with comment text `comment`.

`comment_node:get_comment()`

Return comment string of `comment_node`.

## Class Diagram

`diagram_new(feature_index, range, seqid)`

Return a diagram object which contains the genome nodes given in `feature_index` in the given `range` of the sequence region with sequence ID `seqid`.

`diagram_new_from_array(array, startpos, endpos)`

Return a diagram object which contains the genome nodes given in `array`. The range from `startpos` to `endpos` determines the visible region and should include the nodes in `array`.

## Class FeatureIndex

`feature_index_memory_new()`

Returns a new FeatureIndex object storing the index in memory.

`feature_index:add_gff3file(gff3file)`

Add all features from all sequence regions contained in `gff3file` to `feature_index`.

`feature_index:add_region_node(region_node)`

Add `region_node` to `feature_index`.

`feature_index:add_feature_node(feature_node)`

Add `feature_node` to `feature_index`, implicitly creating sequence region if not present before.

`feature_index:get_features_for_seqid(seqid)`

Returns the feature nodes for sequence ID `seqid` in an array.

`feature_index:get_features_for_range(seqid, range)`

Returns the genome features for sequence ID `seqid` within `range` in an array.

`feature_index:get_first_seqid()`

Returns the first sequence ID stored in `feature_index`.

`feature_index:get_seqids()`

Returns an array containins all sequence IDs stored in `feature_index`.

`feature_index:get_range_for_seqid(seqid)`

Returns the range covered by features of sequence ID `seqid` in `feature_index`.

`feature_index:get_coverage(seqid, maxdist)`

Computes the coverage for the sequence ID `seqid`. The optional `maxdist` parameter denotes the maximal distance two features can be apart without creating a new Range. Returns an array of Ranges denoting parts the of `seqid` covered by features.

`feature_index:get_marked_regions(seqid, maxdist)`

Returns an array of Ranges denoting parts of `seqid` which are covered by at least one marked feature. Internally, `get_coverage()` is called and the `maxdist` is passed along.

`feature_index:render_to_png(seqid, range, png_file, width)`

Render to PNG file `png_file` for `seqid` in `range` with optional `width`. If no `png_file` is given `os.tmpname()` is called to create one. Returns name of written PNG file.

`feature_index:show_seqids()`

Show all sequence IDs.

`feature_index:get_all_features()`

Returns all features from `feature_index`.

## Class FeatureNode

`feature_node_new(seqid, type, startpos, endpos, strand)`

Create a new feature node on sequence with ID `seqid` and type `type` which lies from `startpos` to `end` on strand `strand`. `startpos` and `endpos` always refer to the forward strand, therefore `startpos` has to be smaller or equal than `endpos`.

`feature_node:get_strand()`

Returns the strand of `feature_node`.

`feature_node:get_source()`

Returns the source of `feature_node`.

`feature_node:set_source(source)`

Set the source of `feature_node` to `source`.

`feature_node:get_score()`

Returns the score of `feature_node`.

`feature_node:get_phase()`

Returns the phase of `feature_node`.

`feature_node:get_type()`

Return type of `feature_node` as string.

`feature_node:set_type(type)`

Sets type of `feature_node` to be `type`.

`feature_node:get_attribute(attrib)`

Returns the `attrib` attribute of `feature_node`.

`feature_node:set_attribute(attrib, value)`

Sets the `attrib` attribute of `feature_node` to `value`.

`feature_node:add_attribute(attrib, value)`

Adds the new `attrib` attribute of `feature_node` with value `value`.

`feature_node:remove_attribute(attrib)`

Removes the `attrib` attribute of `feature_node`.

`feature_node:attribute_pairs()`

Returns an Lua iterator over the all attributes of `feature_node`, which delivers pairs of key/value strings. Similar to the Lua `pairs()` function, applied to a table with string keys.

`feature_node:get_exons()`

Returns an array containing the exons of `feature_node`.

`feature_node:children()`

Returns an depth-first Lua iterator over the all children of `feature_node` (including `feature_node` itself).

`feature_node:get_children()`

Returns an depth-first Lua iterator over the all children of `feature_node` (including `feature_node` itself).

`feature_node:direct_children()`

Returns an Lua iterator over the all direct children of `feature_node` (not including `feature_node` itself).

`feature_node:get_direct_children()`

Returns an Lua iterator over the all direct children of `feature_node` (not including `feature_node` itself).

`feature_node:has_child_of_type(type)`

Returns `true` if `feature_node` has a child node of type `type`.

`feature_node:add_child(child)`

Adds `child` as a child node of `feature_node`.

`feature_node:remove_leaf(leaf)`

Removes `leaf` as a child node in the subgraph beneath `feature_node`, if it is a leaf.

`feature_node:output_leading()`

Show leading part of GFF3 output for `feature_node`

`feature_node:extract_sequence(type, join, region_mapping)`

Extract the sequence of `feature_node`. If `join` is false and `feature_node` has type `type` the sequence is returned (using `region_mapping` to get it). If `join` is true and `feature_node` has children of type `type` their joined sequences are returned. If none of the above applies nil is returned.

`feature_node:extract_and_translate_sequence(type, join, region_mapping)`

Extract the translated sequence of `feature_node`. If `join` is false and `feature_node` has type `type` the sequence is returned (using `region_mapping` to get it). If `join` is true and `feature_node` has children of type `type` their joined sequences are returned. If none of the above applies nil is returned.

## Class FeatureNodeIterator

`feature_node_iterator_new(node)`

Returns a new feature node iterator which performs a depth-first traversal of `node` (including `node` itself).

`feature_node_iterator_new_direct(node)`

Returns a new feature node iterator wich iterates over all direct children of `node` (without `node` itself).

`feature_node_iterator:next()`

Returns the next node for `feature_node_iterator` or nil.

## Class FeatureStream

`feature_stream_new(in_stream, feature_index)`

Returns a new feature stream object (a genome stream) over `feature_index` which uses the genome stream `in_stream` as input. That is, all genome nodes which are pulled through the feature stream are added to the `feature_index`.

## Class FeatureVisitor

`feature_visitor_new(feature_index)`

Returns a new feature visitor object over `feature_index`. That is, all genome nodes which are visited by the feature visitor are added to the `feature_index`.

## Class GFF3InStream

`gff3_in_stream_new_sorted(filename)`

Returns a new GFF3 input stream object for `filename`. The file `filename` has to be a sorted GFF3 file. If `filename` is omitted or `nil`, input will be read from standard input.

## Class GFF3OutStream

`gff3_out_stream_new(genome_stream)`

Returns a new GFF3 output stream which pulls its features from `genome_stream`.

## Class GFF3Visitor

`gff3_visitor_new()`

Returns a new GFF3 visitor.

## Class GenomeNode

`genome_node:get_filename()`

Returns the filename of `genome_node`.

`genome_node:get_line_number()`

Returns the line number of `genome_node`.

`genome_node:get_range()`

Returns the range of `genome_node`.

`genome_node:set_range(range)`

Sets the range of `genome_node` to `range`.

`genome_node:get_seqid()`

Returns the sequence id of `genome_node`.

`genome_node:accept(genome_visitor)`

Accept `genome_visitor`.

`genome_node:is_part_of_genome_node(child_node)`

Make `genome_node` the parent of `child_node`.

`genome_node:mark()`

Mark `genome_node`.

`genome_node:is_marked()`

Returns true if `genome_node` is marked, false otherwise.

`genome_node:contains_marked()`

Returns true if `genome_node` contains a marked node, false otherwise.

`genome_node:show(gff3_visitor)`

Show genome node on stdout (using the optional `gff3_visitor`).

`genome_node:show_marked()`

Show marked parts of genome node on stdout.

## Class GenomeStream

`genome_stream:next_tree()`

Returns the next genome node for `genome_stream` or nil.

## Class Imageinfo

`imageinfo_new()`

returns a new ImageInfo object.

`imageinfo:get_recmaps()`

returns an array of tables with the fields "nw_x","nw_y","se_x","se_y" and "feature_ref" with the top left and bottom right coordinates in pixels or points and a GenomeNode reference per element drawn.

## Class Layout

`layout_new(diagram, width)`

Return a Layout object which represents a layout of the content of `diagram` with width `width`.

`layout:get_height(layout)`

Return the height of the resulting `layout`.

`layout:sketch(layout, canvas)`

Draw the content of the `layout` on a given `canvas`.

## Class MetaNode

`meta_node_new(directive, data)`

Returns a new region node with key `directive` and data string `data`.

`meta_node:get_directive()`

Return directive of `meta_node` as string.

`meta_node:get_data()`

Return data of `meta_node` as string.

## Class Range

`range_new(startpos, endpos)`

Returns a new range object with start `startpos` and end `endpos`. `startpos` must be smaller or equal than `endpos`.

`range:get_start()`

Returns start of `range`.

`range:get_end()`

Returns end of `range`.

`range:overlap(other_range)`

Returns true if `range` and `other_range` overlap, false otherwise.

`range:overlap_delta(other_range, delta)`

Returns true if `range` and `other_range` overlap with delta `delta`, false otherwise.

`range:length()`

Returns the length of `range`.

`range:contains(other_range)`

Returns true if `range` contains `other_range`, false otherwise.

`range:join(other_range)`

Returns a new range consisting of `range` and `other_range` joined.

`range:within(point)`

Returns true if `point` lies within `range`, false otherwise.

`ranges_sort(range_array)`

Returns an array containing the ranges from array `range_array` in sorted order.

`ranges_are_sorted(range_array)`

Returns true if the ranges in array `range_array` are sorted, false otherwise.

`range:show()`

Show range on stdout.

## Class RegionMapping

`region_mapping_new_seqfile(seqfile)`

Returns a new region mapping which maps everything onto sequence file `seqfile`.

`region_mapping:get_sequence(seqid, start, end)`

Use `region_mapping` to extract the sequence from `start` to `end` of the given sequence ID `seqid`.

## Class RegionNode

`region_node_new(seqid, range)`

Returns a new region node for sequence id `seqid` spanning `range`.

## Class ScoreMatrix

`score_matrix_new_read_protein(path)`

Returns a new protein score matrix object which has been read from file `path`.

`score_matrix_new_read(path, alphabet)`

Read in score matrix from `path` over given `alphabet` and return it.

`score_matrix:get_dimension()`

Returns the dimension of the `score_matrix` as number.

`score_matrix:get_score(idx1, idx2)`

Returns the score for `idx1`,`idx2` as number.

`score_matrix:show()`

Show `score_matrix` on stdout.

## Class SequenceNode

`sequence_node_new(desc, sequence)`

Returns a new sequence node with description `desc` and (unencoded) sequence `sequence`.

`sequence_node:get_description()`

Returns description of `sequence_node`.

`sequence_node:get_sequence()`

Returns sequence of `sequence_node`.

`sequence_node:get_sequence_length()`

Returns length of the sequence of `sequence_node`.

## Class StreamEvaluator

`stream_evaluator_new(reality_stream, prediction_stream)`

Returns a new stream evaluator object for the two genome streams `reality_stream` and `prediction_stream`.

`stream_evaluator:evaluate(genome_visitor)`

Run evaluation of `stream_evaluator`. All evaluated features are visited by the optional `genome_visitor`.

`stream_evaluator:show()`

Show result of `stream_evaluator` on stdout.

## Class translate

`translate_dna(dna)`

Returns translated `dna`.

## Index

`alphabet:add_mapping`
`alphabet:add_wildcard`
`alphabet:decode`
`alphabet:size`
`alphabet_new_dna`
`alphabet_new_empty`
`alphabet_new_protein`
`bittab:and_equal`
`bittab:bit_is_set`
`bittab:complement`
`bittab:equal`
`bittab:set_bit`
`bittab:unset_bit`
`bittab_new`
`canvas:to_file`
`canvas_cairo_file_new_pdf`
`canvas_cairo_file_new_png`
`canvas_cairo_file_new_ps`
`canvas_cairo_file_new_svg`
`cds_stream_new`
`comment_node:get_comment`
`comment_node_new`
`csa_stream_new`
`diagram_new`
`diagram_new_from_array`
`display`
`export`
`feature_index:add_feature_node`
`feature_index:add_gff3file`
`feature_index:add_region_node`
`feature_index:get_all_features`
`feature_index:get_coverage`
`feature_index:get_features_for_range`
`feature_index:get_features_for_seqid`
`feature_index:get_first_seqid`
`feature_index:get_marked_regions`
`feature_index:get_range_for_seqid`
`feature_index:get_seqids`
`feature_index:render_to_png`
`feature_index:show_seqids`
`feature_index_memory_new`
`feature_node:add_attribute`
`feature_node:add_child`
`feature_node:attribute_pairs`
`feature_node:children`
`feature_node:direct_children`
`feature_node:extract_and_translate_sequence`
`feature_node:extract_sequence`
`feature_node:get_attribute`
`feature_node:get_children`
`feature_node:get_direct_children`
`feature_node:get_exons`
`feature_node:get_phase`
`feature_node:get_score`
`feature_node:get_source`
`feature_node:get_strand`
`feature_node:get_type`
`feature_node:has_child_of_type`
`feature_node:output_leading`
`feature_node:remove_attribute`
`feature_node:remove_leaf`
`feature_node:set_attribute`
`feature_node:set_source`
`feature_node:set_type`
`feature_node_iterator:next`
`feature_node_iterator_new`
`feature_node_iterator_new_direct`
`feature_node_new`
`feature_stream_new`
`feature_visitor_new`
`features_contain_marked`
`features_extract_sequences`
`features_get_marked`
`features_mRNAs2genes`
`features_show`
`features_show_marked`
`genome_node:accept`
`genome_node:contains_marked`
`genome_node:get_filename`
`genome_node:get_line_number`
`genome_node:get_range`
`genome_node:get_seqid`
`genome_node:is_marked`
`genome_node:is_part_of_genome_node`
`genome_node:mark`
`genome_node:set_range`
`genome_node:show`
`genome_node:show_marked`
`genome_stream:next_tree`
`gff3_in_stream_new_sorted`
`gff3_out_stream_new`
`gff3_visitor_new`
`imageinfo:get_recmaps`
`imageinfo_new`
`layout:get_height`
`layout:sketch`
`layout_new`
`meta_node:get_data`
`meta_node:get_directive`
`meta_node_new`
`rand_max`
`range:contains`
`range:get_end`
`range:get_start`
`range:join`
`range:length`
`range:overlap`
`range:overlap_delta`
`range:show`
`range:within`
`range_new`
`ranges_are_sorted`
`ranges_sort`
`re`
`region_mapping:get_sequence`
`region_mapping_new_seqfile`
`region_node_new`
`reload`
`score_matrix:get_dimension`
`score_matrix:get_score`
`score_matrix:show`
`score_matrix_new_read`
`score_matrix_new_read_protein`
`sequence_node:get_description`
`sequence_node:get_sequence`
`sequence_node:get_sequence_length`
`sequence_node_new`
`show`
`show_table`
`stream_evaluator:evaluate`
`stream_evaluator:show`
`stream_evaluator_new`
`translate_dna`